Hi,
Yes, masking within an image (including zeros within the image) can impose artificial boundaries that would bias registration. Taking an ROI by reducing the size of the image FOV (throwing away voxels, rather than replace them with zeros) is fine and does not cause problems (as the registration methods only use the overlapping FOV portions of the images for all calculations).
What the problem is most likely to be caused by is the lack of brain to non-brain boundary in the image. We strongly discourage the use of the brain mask as a weighting image, since it removes the information about where the brain edge is (since the transition from brain to non-brain never occurs, as all the non-brain voxels are outside of the mask and hence ignored). So I would just avoid masking like this. If you need to mask for some other reason (e.g. to avoid pathology) then that is fine, although small masks can cause problems for the mutual information measures, as they use 2D histograms to calculate their values, and these histograms are more influenced by small numbers of voxels (giving poor estimates of the values per bin) than for any of the other measures (that use 1D histograms, or no histograms).
All the best,
Mark
On 7 Apr 2014, at 18:06, "Dewey, Blake (NIH/NINDS) [F]" <[log in to unmask]> wrote:
> Wouldn't that impose an artificial boundary on the image for the registration?
>
> Blake
>
> From: David Grayson <[log in to unmask]<mailto:[log in to unmask]>>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>>
> Date: Monday, April 7, 2014 1:02 PM
> To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>
> Subject: Re: [FSL] FLIRT using Weighting Image and Mutual Information
>
> Hi Blake,
>
> For MI, you can try explicitly masking your images with fslmaths prior to registration.
>
> Best,
>
> David
>
>
> On Mon, Apr 7, 2014 at 8:05 AM, Blake Dewey <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> I have been trying to use weighted registration for my structural image (using the brain mask as a weighting image). I have had success with each of the cost functions except for the mutual information and normalized mutual information functions. For these two cost function the registration fails spectacularly, often rotating the image out of the FOV. Is there a reason for this? What can I use if I have two very different contrasts to register in this way?
>
> Blake
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